1. Field of the Invention
This invention relates generally to nucleic acid sequences encoding members of the mPing/Pong family of transposable elements. In addition, this invention relates to nucleic acid sequences encoding polypeptides that function as transposases, or polypeptides that interact with transposases to modulate the transposition of members of the mPing/Pong genus of transposable elements.
2. Background Art
Rice is the most important crop for human nutrition in the world. At 430 Mb, rice also has the smallest genome among the agriculturally important cereals, including the genomes of maize, sorghum, barley and wheat (Arumuganathan & Earle, 1991 Plant Mol. Biol., 9: 208-218). For these reasons rice is the focus of several genome sequencing projects in both the public and private sectors (Burr, 2002 Plant Cell, 14: 521-523; Goff, et al., 2002 Science, 296: 92-100; Yu, et al., 2002 Science, 296: 79-92). Computer-assisted analyses of rice genomic sequence indicate that despite its small size, over 40% of the genome is repetitive DNA; most of this is related to transposable elements (Goff, et al., 2002 Science, 296: 92-100; Yu, et al., 2002 Science, 296: 79-92). Although the largest component of transposable elements in the rice genome is class 1 LTR retrotransposons (14%), the largest group with over 100,000 elements divided into hundreds of families is miniature inverted-repeat transposable elements (MITEs), comprising about 6% of the genome (Tarchini et al., 2000 Plant Cell, 12: 381-391; Jiang & Wessler, 2001 Plant Cell, 13: 2553-2564). MITEs are the predominant transposable element associated with the noncoding regions of the genes of flowering plants, especially the grasses and have been found in several animal genomes including nematodes, mosquitoes, fish, and humans (reviewed in Feschotte et al., 2002 Nat. Rev. Genet., 3: 329-341).
MITEs are structurally reminiscent of nonautonomous DNA (class 2) elements with their small size (less than 600 bp) and short (10 to 30 bp) terminal inverted repeat (TIR). However, their high copy number (up to 10,000 copies/family) and target-site preference for TA or TAA distinguish them from most previously described nonautonomous DNA elements (Feschotte et al., 2002 Nat., Rev. Genet., 3: 329-341). Nonautonomous elements, which make up a significant fraction of eukaryotic genomes, have been classified into families based on the transposase responsible for their mobility. Classifying MITEs in this way has been problematic because no actively transposing MITE had been reported in any organism. Instead, based on the similarity of their TIRs and their target site duplication (TSD), most of the tens of thousands of plant MITEs have been classified into two superfamilies: Tourist-like MITEs and Stowaway-like MITEs (Jiang & Wessler, 2001 Plant Cell, 13: 2553-2564; Turcotte et al., 2001 Plant J., 25: 169-179; Feschotte & Wessler, 2002 Proc. Natl. Acad. Sci. USA, 99: 280-285). Recently, evidence has accumulated linking Tourist and Stowaway MITEs with two superfamilies of transposases, PIF/IS5 and Tc1/mariner, respectively (Turcotte et al., 2001 Plant J., 25: 169-179; Feschotte & Wessler, 2002 Proc. Natl. Acad. Sci. USA, 99: 280-285; Zhang, et al., Proc. Natl. Acad. Sci. USA, 98: 12572-12577).
Activity has not been demonstrated for any of the hundreds of MITE families previously identified in the rice genome, however three families of LTR retrotransposons, Tos10, Tos17, and Tos19, have been shown to transpose in both japonica (Nipponbare) and indica (C5924) cell culture (Hirochika, et al., 1996 Proc. Natl. Acad. Sci. USA, 93: 7783-7788). Similarly, no activity has been associated with the hundreds of MITE families from either plants or animals. Most MITE families are characterized by high copy number (hundreds to thousands per haploid genome) and intra-family sequence identity that is rarely over 95% (Feschotte & Wessler, 2002 Proc. Natl. Acad. Sci. USA, 99: 280-285). Since newly amplified elements are usually identical, these families have most likely been inactive for hundreds of thousands or even millions of years. In addition, to date, only a single active DNA transposon, Tol2, has been isolated from a vertebrate (Kawakami, et al., 2000 Proc. Natl. Acad. Sci. USA, 97: 11403-8), and no active DNA transposons have been isolated from mammals.
Because no activity has been demonstrated for any of the known MITE families in either plants or animals, there is a need in the art to identify MITEs and related transposable elements that are actively transposing.